[2024-01-24 12:06:21,923] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:21,926] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:21,926] [INFO] DQC Reference Directory: /var/lib/cwl/stg94426b76-324a-4194-ad6d-6f281c41404b/dqc_reference
[2024-01-24 12:06:23,143] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:23,145] [INFO] Task started: Prodigal
[2024-01-24 12:06:23,145] [INFO] Running command: gunzip -c /var/lib/cwl/stgcbb1b9c1-57a7-4643-9163-77daa5cf5522/GCF_006968745.1_ASM696874v1_genomic.fna.gz | prodigal -d GCF_006968745.1_ASM696874v1_genomic.fna/cds.fna -a GCF_006968745.1_ASM696874v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:42,299] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:42,299] [INFO] Task started: HMMsearch
[2024-01-24 12:06:42,299] [INFO] Running command: hmmsearch --tblout GCF_006968745.1_ASM696874v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94426b76-324a-4194-ad6d-6f281c41404b/dqc_reference/reference_markers.hmm GCF_006968745.1_ASM696874v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:42,674] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:42,675] [INFO] Found 6/6 markers.
[2024-01-24 12:06:42,735] [INFO] Query marker FASTA was written to GCF_006968745.1_ASM696874v1_genomic.fna/markers.fasta
[2024-01-24 12:06:42,736] [INFO] Task started: Blastn
[2024-01-24 12:06:42,736] [INFO] Running command: blastn -query GCF_006968745.1_ASM696874v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94426b76-324a-4194-ad6d-6f281c41404b/dqc_reference/reference_markers.fasta -out GCF_006968745.1_ASM696874v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:43,291] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:43,295] [INFO] Selected 14 target genomes.
[2024-01-24 12:06:43,296] [INFO] Target genome list was writen to GCF_006968745.1_ASM696874v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:43,302] [INFO] Task started: fastANI
[2024-01-24 12:06:43,302] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbb1b9c1-57a7-4643-9163-77daa5cf5522/GCF_006968745.1_ASM696874v1_genomic.fna.gz --refList GCF_006968745.1_ASM696874v1_genomic.fna/target_genomes.txt --output GCF_006968745.1_ASM696874v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:07,209] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:07,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94426b76-324a-4194-ad6d-6f281c41404b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:07,209] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94426b76-324a-4194-ad6d-6f281c41404b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:07,220] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:07,221] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:07,221] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Brasilonema sennae	strain=CENA114	GCA_006968745.1	1397703	1397703	type	True	100.0	2739	2741	95	conclusive
Brasilonema bromeliae	strain=SPC951	GCA_012912135.1	383615	383615	type	True	90.6279	1510	2741	95	below_threshold
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	78.0349	816	2741	95	below_threshold
Scytonema hofmannii	strain=PCC 7110	GCA_000346485.2	34078	34078	type	True	77.9563	926	2741	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	77.6695	690	2741	95	below_threshold
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	77.5402	691	2741	95	below_threshold
Aetokthonos hydrillicola	strain=CCALA 1050	GCA_017591665.1	1550245	1550245	type	True	77.3246	558	2741	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	77.3214	611	2741	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	77.278	622	2741	95	below_threshold
Fischerella thermalis	strain=PCC 7521	GCA_000317225.1	372787	372787	type	True	77.2627	541	2741	95	below_threshold
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	76.8936	385	2741	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	76.8388	382	2741	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:07,223] [INFO] DFAST Taxonomy check result was written to GCF_006968745.1_ASM696874v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:07,224] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:07,224] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:07,224] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94426b76-324a-4194-ad6d-6f281c41404b/dqc_reference/checkm_data
[2024-01-24 12:07:07,226] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:07,297] [INFO] Task started: CheckM
[2024-01-24 12:07:07,297] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006968745.1_ASM696874v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006968745.1_ASM696874v1_genomic.fna/checkm_input GCF_006968745.1_ASM696874v1_genomic.fna/checkm_result
[2024-01-24 12:08:03,953] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:03,954] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:03,978] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:03,979] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:03,979] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006968745.1_ASM696874v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:03,979] [INFO] Task started: Blastn
[2024-01-24 12:08:03,979] [INFO] Running command: blastn -query GCF_006968745.1_ASM696874v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94426b76-324a-4194-ad6d-6f281c41404b/dqc_reference/reference_markers_gtdb.fasta -out GCF_006968745.1_ASM696874v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:04,727] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:04,732] [INFO] Selected 9 target genomes.
[2024-01-24 12:08:04,732] [INFO] Target genome list was writen to GCF_006968745.1_ASM696874v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:04,740] [INFO] Task started: fastANI
[2024-01-24 12:08:04,741] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbb1b9c1-57a7-4643-9163-77daa5cf5522/GCF_006968745.1_ASM696874v1_genomic.fna.gz --refList GCF_006968745.1_ASM696874v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006968745.1_ASM696874v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:27,865] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:27,873] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:27,874] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_006968915.1	s__Brasilonema octagenarum	99.9741	2721	2741	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Brasilonema	95.0	99.69	99.40	0.99	0.99	3	conclusive
GCF_017982655.1	s__Brasilonema sp017982655	94.2196	2009	2741	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Brasilonema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012912135.1	s__Brasilonema bromeliae	90.596	1513	2741	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Brasilonema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828085.3	s__Brasilonema tolypothrichoides	89.9861	1925	2741	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Brasilonema	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012031965.1	s__Brasilonema sp012031965	85.5321	1525	2741	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Brasilonema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012912105.1	s__Brasilonema sp012912105	85.1772	1695	2741	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Brasilonema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368235.1	s__Tolypothrix_B sp002368235	82.8932	1700	2741	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Tolypothrix_B	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000315565.1	s__Mastigocladopsis repens	82.4317	1419	2741	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Mastigocladopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010091925.1	s__Nostoc sp010091925	77.5978	704	2741	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:27,876] [INFO] GTDB search result was written to GCF_006968745.1_ASM696874v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:27,876] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:27,879] [INFO] DFAST_QC result json was written to GCF_006968745.1_ASM696874v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:27,880] [INFO] DFAST_QC completed!
[2024-01-24 12:08:27,880] [INFO] Total running time: 0h2m6s